Research workbench
Crystal structure of adenylate kinase from an extremophilic archaeon aeropyrum pernix with ATP and AMP
Analyse Crystal structure of adenylate kinase from an extremophilic archaeon aeropyrum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LN3
- Type
- protein
- Length
- 202 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase
- EC
- 2.7.4.3
- UniProt
- Q9YDD2
- Ligands
- AMP, ATP, MG, CL
- Pockets
- 1 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylate kinase (EC 2.7.4.3) | protein | 202 | 53% helix, 19% strand | Q9YDD2 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.73 | 0.88 | 42 | AMP, ATP, MG |
Compared structures
- 6LN3 · Crystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9YDD2 · AlphaFold monomer V2.0 prediction for adenylate kinase (Q9YDD2) · a predicted model of the same protein · chain A against A, TM-score 0.93
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9YDD2
- Elsewhere: RCSB PDB 6LN3 · PDBe 6LN3 · UniProt Q9YDD2
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